Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation

Yeast

Volumn 20, Issue 16, 2003, Pages 1369-1385

  Rossignol, Tristan ^a   Dulau, Laurent ^b   Julien, Anne ^b   Blondin, Bruno ^a  

^a CEMAGREF   (France)

^b LALLEMAND SAS   (France)

Author keywords

Alcoholic fermentation; Microarrays; Stress; TOR pathway; Transcriptome; Wine yeast

Indexed keywords

ALCOHOL; AMINO ACID TRANSFER RNA LIGASE; CELL MEMBRANE PROTEIN; CYTOPLASM PROTEIN; MITOCHONDRIAL PROTEIN; NITROGEN; RIBOSOME PROTEIN; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; EXHAUSTION; FERMENTATION MEDIUM; FERMENTATION MONITORING; FUNGAL STRAIN; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE TARGETING; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME; GROWTH INHIBITION; NITROGEN UTILIZATION; NONHUMAN; NUTRITION; PRIORITY JOURNAL; PROTEIN FUNCTION; SIGNAL TRANSDUCTION; STARVATION; STRESS; YEAST;

ETHANOL; FERMENTATION; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; GLYCOGEN; KINETICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC; TREHALOSE; WINE;

EID: 0346882674     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.1046     Document Type: Article

References (58)

1. Abramova NE, Cohen BD, Sertil O, et al. 2001. Regulatory mechanisms controlling expression of the DAN/TIR mannoprotein genes during anaerobic remodeling of the cell wall in Saccharomyces cerevisiae. Genetics 157: 1169-1177.
2. Alexandre H, Rousseaux I, Charpentier C. 1994. Ethanol adaptation mechanisms in Saccharomyces cerevisiae. Biotechnol Appl Biochem 20: 173-183.
3. Alexandre H, Ansanay-Galeote V, Dequin S, Blondin B. 2001. Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett 498: 98-103.
4. Backhus LE, DeRisi J, Brown PO, Bisson LF. 2001. Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Res 1413: 1-15.
5. Bakalinsky AT, Snow R, 1990. The chromosomal constitution of wine strains of Saccharomyces cerevisiae. Yeast 6: 367-382.
6. Bataillon M, Rico A, Sablayrolles JM, Salmon JM, Barre P. 1996. Early thiamine assimilation by yeasts in enological conditions: impact on alcoholic fermentation kinetics. J Ferment Bioeng 82: 101-106.
7. Bauer FF, Pretorius IS. 2000. Yeast stress response and fermentation efficiency: how to survive the making of wine - a review. S Afr J Enol 21: 27-51.
8. Beck T, Hall MN. 1999. The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402: 689-692.
9. Bely L, Sablayrolles J, Barre P. 1990. Description of alcoholic fermentation kinetics: its variability and significance. Am J Enol Viticult 40: 319-324.
10. Bidenne C, Blondin B, Dequin S, Vezinhet F. 1992. Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae. Curr Genet 22: 1-7.
11. Blomberg A. 2000. Metabolic surprises in Saccharomyces cerevisiae during adaptation to saline conditions: questions, some answers and a model. FEMS Microbiol Lett 182: 1-8.
12. Cardenas ME, Cutler NS, Lorenz MC, Di Como CJ, Heitman J. 1999. The TOR signaling cascade regulates gene expression in response to nutrients. Genes Dev 13: 3271-3279.
13. Causton HC, Ren B, Koh SS, et al. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323-337.
14. Cavalieri D, Townsend JP, Hartl DL. 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci USA 97: 12 369-12 374.
15. de Groot F, Bebelman JP, Mager WH, Planta RJ. 2000. Very low amounts of glucose cause repression of the stress-responsive gene HSP12 in Saccharomyces cerevisiae. Microbiology 146: 367-375.
16. de Winde JH, Thevelein JM, Winderickx J. 1997. From feast to famine: adaptation to nutrient depletion in yeast. In Yeast Stress Responses, Hohmann S, Mager WH (eds). R.G. Landes: Austin, USA; 7-52.
17. Delneri D, Gardner DC, Oliver SG. 1999. Analysis of the seven-member AAD gene set demonstrates that genetic redundancy in yeast may be more apparent than real. Genetics 153: 1591-1600.
18. DeRisi JL, Iyer VR, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
19. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14 863-14 868.
20. Estruch F. 2000. Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol Rev 24: 469-486.
21. Fleet GH, Heard GM. 1993. Yeasts - growth during fermentation. In Wine Microbiology and Biotechnology, Fleet GH (ed.). Harwood Academic: Chur, Switzerland; 27-54.
22. Francois J, Parton JL. 2001. Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 25: 125-145.
23. Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
24. 2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 12: 586-597.
25. Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL. 1999. Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA 96: 14 866-14 870.
26. Hauser NC, Fellenberg K, Gil R, et al. 2001. Whole genome analysis of a wine yeast strain. Comp Funct Genom 2: 69-79.
27. Henscke P, Jiranek V 1993. Yeasts - metabolism of nitrogen compounds. In Wine Microbiology, Biotechnology, Fleet GH. (ed.). Harwood Academic: Chur, Switzerland; 77-164.
28. Hohmann S. 2002. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66: 300-372.
29. Holstege FC, Jennings EG, Wyrick JJ, et al. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
30. Ibeas JI, Jimenez J. 1996. Genomic complexity and chromosomal rearrangements in wine-laboratory yeast hybrids. Curr Genet 30: 410-416.
31. Jiranek V, Langridge P, Henschke PA. 1995. Regulation of hydrogen sulfide liberation in wine-producing Saccharomyces cerevisiae strains by assimilable nitrogen. Appl Environ Microbiol 61: 461-467.
32. Kudo M, Vagnoli P, Bisson LF. 1998. Imbalance of pH and potassium concentration as a cause of stuck fermentations. Am J Enol Viticult 49: 295-301.
33. Kuruvilla FG, Shamji AF, Schreiber SL. 2001. Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc Natl Acad Sci USA 98: 7283-7288.
34. Kwast KE, Lai LC, Menda N, et al. 2002. Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J Bacteriol 184: 250-265.
35. Llorente B, Durrens P, Malpertuy A, et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae. FEBS Lett 487: 122-133.
36. Llorente B, Fairhead C, Dujon B. 1999. Genetic redundancy and gene fusion in the genome of the baker's yeast Saccharomyces cerevisiae: functional characterization of a three-member gene family involved in the thiamine biosynthetic pathway. Mol Microbiol 32: 1140-1152.
37. Mortimer RK. 2000. Evolution and variation of the yeast (Saccharomyces) genome. Genome Res 10: 403-409.
38. 1-S transition. EMBO J 19: 1613-1624.
39. Perez-Ortin JE, Garcia-Martinez J, Alberola TM. 2002. DNA chips for yeast biotechnology. The case of wine yeasts. J Biotechnol 98: 227-241.
40. Perez-Torrado R, Carrasco P, Aranda A, et al. 2002. Study of the first hours of microvinification by the use of osmotic stress-response genes as probes. Syst Appl Microbiol 25: 153-161.
41. Praekelt UM, Byrne KL, Meacock PA. 1994. Regulation of THI4 (MOL1), a thiamine-biosynthetic gene of Saccharomyces cerevisiae. Yeast 10: 481-490.
42. Pretorius IS. 2000. Tailoring wine yeast for the new millennium: novel approaches to the ancient art of wine making. Yeast 16: 675-729.
43. Puig S, Perez-Ortin JE. 2000. Stress response and expression patterns in wine fermentations of yeast genes induced at the diauxic shift. Yeast 16: 139-148.
44. Rachidi N, Barre P, Blondin B. 1999. Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850.
45. Rachidi N, Martinez MJ, Barre P, Blondin B. 2000. Saccharomyces cerevisiae PAU genes are induced by anaerobiosis. Mol Microbiol 35: 1421-1430.
46. Regenberg B, During-Olsen L, Kielland-Brandt MC, Holmberg S. 1999. Substrate specificity and gene expression of the amino acid permeases in Saccharomyces cerevisiae. Curr Genet 36: 317-328.
47. Remize F, Andrieu E, Dequin S. 2000. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae: role of the cytosolic Mg(2+) and mitochondrial K(+) acetaldehyde dehydrogenases Ald6p and Ald4p in acetate formation during alcoholic fermentation. Appl Environ Microbiol 66: 3151-3159.
48. Riou C, Nicaud JM, Barre P, Gaillardin C. 1997. Stationary-phase gene expression in Saccharomyces cerevisiae during wine fermentation. Yeast 13: 903-915.
49. Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, et al. 2002. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast 19: 1261-1276.
50. Roustan J, Sablayrolles J. 2002. Trehalose and glycogen in wine-making yeasts: methodological aspects and variability. Biotechnol Lett 24: 1059-1064.
51. Sablayrolles JM. 1996. Effectiveness of combined ammoniacal nitrogen and oxygen additions for completion of sluggish and stuck fermentations. J Ferment Bioeng 82: 337-381.
52. Schmelzle T, Hall MN. 2000. TOR, a central controller of cell growth. Cell 103: 253-262.
53. Spellman PT, Sherlock G, Zhang MQ, et al. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
54. Thomas D, Surdin-Kerjan Y. 1997. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61: 503-532.
55. Trabalzini L, Paffetti A, Scaloni A, et al. 2003. Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae. Biochem J 370: 35-46.
56. Tseng GC, Oh MK, Roblin L, Liao JC, Wong WH. 2001. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29: 2549-2557.
57. Werner-Washburne M, Braun E, Johnston GC, Singer RA. 1993. Stationary phase in the yeast Saccharomyces cerevisiae. Microbiol Rev 57: 383-401.
58. Wilcox LJ. Balderes DA, Wharton B, et al. 2002. Transcriptional profiling identifies two members of the ATP-binding-cassette transporter superfamily required for sterol uptake in yeast. J Biol Chem 277: 32 466-32 472.